Modules

Modules can be turned on and off for an OpenBioMaps project. The basic functions of the system are supplemented with various functions (such as text search options). Modules can be defined per table and assigned to different users or user groups. The locations of the modules are as follows:

• map page

• profile tab

Most modules can be configured with simple parameters, but some modules have a custom configuration interface.

Modul administration:

The modules can be enabled and configured on the project_administration -> modules page.

Add a module

Module access

Drop a module

Turn off a module

Custom modules

Parameters for modules

Module descriptions

additional_columns

Additional columns

Calls:

Functions: return_columns()

General description:
    use it together with the join_tables module
    return with an array:
    co [0] columns array
    c  [1] column name assoc array

Parameters: New line separated list of column names

allowed_columns

Columns visibility for users in different access levels
It depends on the existence of _rules table

Calls:

Functions:
   return_columns(), return_gcolumns()

General description:

Parameters:
   for_sensitive_data: comma separated list of column names
   for_no-geom_data: comma separated list of column names
   for_general: comma separated list of column names

bold_yellow

Bold yellow text for some columns in the results lists.

Calls:

General description:

Parameters:
  New line separated list of column names

box_load_selection

Map filter functions

These functions returns with a html table which displayed beside the map window
These are optional boxes. Setting are in the biomaps db projects' table.

Load prevously saved spatial queries' polygons

Calls:

General description:

Parameters:

    available spatial relationships (optional, if no parameter is given, all relationships are available)
        contains
        intersects
        crosses
        disjoint

box_load_coord

Show given coordinates position on the map

Calls: print_box, limits, ajax, print_js

General description:

Parameters: example:

{
  "wgs84":"4326",
  "eov":"23700"
 }

box_load_last_data

Query last data or last uploads.

Calls:

General description:

Parameters: Number of records in last uploads, default is 10

box_custom

Custom box - only user defined version exists.

Calls:

General description: The custom module has to be in includes/modules/private/ folder (You have to create private folder, if it's not there. It is recomended to add read-only permissions for www-data user to avoid the deletion or modification of the custom module in the course of a system upgrade.

Parameters: a file's basename in includes/modules/private folder. E.g. hrsz_query

Where hrsz_query_Class is a class in hrsz_query.php in includes/modules/private/ folder.

This Class should include at least print_box() and print_js() functions.

photos

Photo or other attachment box.

Calls:

General description:

Parameters:

read_table

Present a SQL table or an SQL view as a rollable html table. This table is available through a unique link.

Calls: mainpage/gridbox

General description:

Parameters:
 [{"table":"schema.table",
   "label":"somesthing",
   "orderby":"column"}, ... ]

results_summary

Summary of results.

results_table

Create a full html table of the results.

Calls:

General description:
    Not used!!

Parameters:

results_asList

Create foldable slides like results.

Calls: results_builder()

General description:

Parameters:

results_asGPX

Save results as a GPX file.

Calls:

General description:

Parameters:

results_asCSV

Save results as a csv file.

Hívások:

Általános leírás:

Paraméterek:

results_asJSON

Save results as a JSON file.

Calls:

General description:

Parameters:

results_asSHP

Results can be saved as SHP files. Separate files are created for the different geometry types. These can be downloaded in a zip archive.

Calls:

General description:

Parameters:

results_asKML

Save results as a KML file.

Calls:

General description:

Parameters:

results_buttons

Save and other button above results section, under map.

Calls:

General description:

Parameters:

results_asStable

Compact results table Stable.

Calls:

General description:

Parameters:

specieslist

Specieslist summary above results.

Calls:

General description:

Parameters:

text_filter

Taxon and other text filters.

Calls:

General description:
    create boxes
    assemble WHERE part of query string

Parameters: complex example:

magyar
obm_taxon
megj::colour_rings
obm_datum
obm_uploading_date
obm_uploader_user
d.szamossag:nested(d.egyedszam):autocomplete
d.egyedszam:values():
obm_files_id
faj::autocomplete

text_filter2

Advanced taxon and other text filters.

Calls:

General description:
    create boxes
    assemble WHERE part of query string

Parameters: example:

transform_data

Transform data

Calls:

General description:
    In result list it transform data as need
    E.g. geometry to wkt

Parameters: example:

obm_geometry:geom
obm_uploading_id:uplid
tema:mmm

extra_params

Extra input paramaters for forms.

Calls:

General description:

Parameters:

join_tables

This modules makes possible to display joined data on the data-sheet-page. At the moment it supports only simple LEFT JOINS on one equation.

Calls:

Functions:

load_joined_data()

General description:

Parameters:

[
    {
        "table": "teszt_events",
        "join_on": [
            {
                "ref_field": "obm_id",
                "join_field": "patient_id"
            }
        ]
    },
    {
        "table": "teszt_masik",
        "join_on": [
            {
                "ref_field": "obm_id",
                "join_field": "fid"
            }
        ]
    }
]

shared_geom

If this module is enabled “Manage custom geometries” option will appear on your profile page.

It is possible to upload or draw custom geometries for further action. These action can be make spatial queries or assign geometry to uploaded data.

You can manage the custom geometries in the profile page by following two links: shared geometries and own geometries.

Following the own geometries link you can delete or share, rename and modify the view options of your geometries. The view options are the following: View in spatial selection list and View in upload data - assign named spatial forms list.

Following the shared geometries link you can rename the geometries and modify the view options. You cannot delete the shared geometries!

snap_to_grid

Project specified sanp to grid points on the map

Calls:

Functions: geom_column(), geom_column_join(), rules_join()

General description:
    not recommended to use!

Parameters:

restricted_data

Rule based data restriction

alls

Functions: rule_data()

General description:

Parameters:

identify_point

A tool for identify one or more data elements on the map

Calls:

Functions: return_data(), print_button()

General description:

Parameters:
    column names

    json object: shows a hyperlink.

        elements:

            type - obligatory, egyelőre csak a "link" érték működik

            href - obligatory - hivatkozás címe

            label - obligatory - a link/gomb szövege/cimkéje - többnyelvűséget támogatja

            class - optional - a linkhez rendelt osztályok

            id - optional - a linkhez rendelt azonosító

            target - optional - alapértelmezett "_blank"

            params - optional - a href elem paraméterei

        A href elemet a modul-paraméterek közt felsorolt oszlopok értékeivel paraméterezhetjük. lásd a példát:

        Példa:
        { "type": "link", "href": "//example.com?nest_id=%1%&species=%2%", "label": "str_add_data", "class": "pure-button button-href", "params": ["obm_id","species"] }

        A fenti példa a következő hiperlinket fogja generálni:

        <a href="//example.com?nest_id=2898&species=Brachyramphus perdix" target="_blank" id="" class="pure-button button-href">Adat hozzáadása</a>

        A json-t egy sorosra kell tömöríteni!

    obm_files_id: Displays a photo icon on the popup if the record has an attachment.

notify

Creates custom postgres based notify events.

Calls:

Functions: listen(), unlisten(), notify(), email()

General description:

Parameters:

custom_data_check

Custom data checks of upload data.

Calls:

Functions: list(), check()

General description:

Parameters:

custom_filetype

Custom file preparation. E.g. observado style CSV

Calls:

Functions: option_list(), custom_read()

General description:

Parameters:

create_pg_user

If this module is enabled “Create postgres user” option will appear on your profile page.

Create a restricted access postgres user

Calls:

Functions: create_pg_user(), show_button()

General description:

    By enabling the module (who has the right to use the module), users can create their own postgres user. This user can only read from the database.
    It can read all the data tables assigned to the project.
    It can only connect to a database from one client program at a time.
    After one year, Its access expires automatically.
    Users can renew their access at any time.

Parameters:

grid_view

View data on custom polygon grid. E.g UTM 2.5km, UTM 10KM, KEF grid, snap to grid, ...

Calls:

Functions: print_box(), default_grid_geom(), get_grid_layer()

General description:

Parameters: layer_options

Parameters example: layer_options:kef_5 (dinpi_grid), utm_2.5 (dinpi_grid), utm_10 (dinpi_grid), utm_100 (dinpi_grid), original (dinpi_points,dinpi_grid),etrs(dinpi_grid)


On the nnn_grid table on the comment field the layers visible names should be set:

COMMENT ON COLUMN public.nnn_qgrids.original IS 'original';
COMMENT ON COLUMN public.nnn_qgrids.snap IS 'snap';
COMMENT ON COLUMN public.nnn_qgrids.snap_polygon IS 'snap_polygon';

Example trigger functions:

Trigger on nnn_qgrids. Arguments are in the function:

CREATE TRIGGER update_grid_geoms BEFORE INSERT OR UPDATE ON public.tytoalba_qgrids FOR EACH ROW EXECUTE PROCEDURE public.update_qgrid_geoms_arg('0.1', '0.1', 'f', 'f', 'f', 'f', 't', 't', '0.05');

Trigger on nnn table:

CREATE TRIGGER qgrids BEFORE INSERT OR DELETE OR UPDATE ON public.debrecen_dnabank FOR EACH ROW EXECUTE PROCEDURE insert_originalgeom_into_qgrids()

Function insert_originalgeom_into_qgrids()

BEGIN
  IF tg_op = 'INSERT' THEN
    EXECUTE format('INSERT INTO %I_qgrids (row_id,original) SELECT %L,%L::geometry',TG_TABLE_NAME,NEW.obm_id,NEW.obm_geometry);
    RETURN NEW;
END IF;

  IF tg_op = 'UPDATE' THEN
    EXECUTE format('UPDATE %I_qgrids SET "original"=%L::geometry WHERE row_id=%L', TG_TABLE_NAME,NEW.obm_geometry,NEW.obm_id);
    RETURN NEW;
END IF;

IF tg_op = 'DELETE' THEN
    EXECUTE format('DELETE FROM %I_qgrids WHERE row_id=%L',TG_TABLE_NAME,OLD.obm_id);
    RETURN OLD;
END IF;
END;

Function update_qgrid_geoms_arg()

DECLARE
    snap_x numeric := TG_ARGV[0];
    snap_y numeric := TG_ARGV[1];
    kef5 boolean := TG_ARGV[2];
    kef10 boolean := TG_ARGV[3];
    utm25 boolean := TG_ARGV[4];
    utm10 boolean := TG_ARGV[5];
    snap boolean := TG_ARGV[6];
    snap_polygon boolean := TG_ARGV[7];
    snap_polygon_size numeric := TG_ARGV[8];
BEGIN

IF tg_op = 'UPDATE' THEN
    IF kef5 THEN
        EXECUTE FORMAT('SELECT geometry FROM shared."kef_5x5" WHERE st_within(%L::geometry,geometry)',NEW.original) INTO NEW."kef_5";
    END IF;
    IF kef10 THEN
        EXECUTE FORMAT('SELECT geometry FROM shared."kef_10x10" WHERE st_within(%L::geometry,geometry)',NEW.original) INTO NEW."kef_10";
    END IF;
    IF utm25 THEN
        EXECUTE FORMAT('SELECT st_transform(geometry,4326) as geom FROM shared."utm_2.5x2.5" WHERE st_within(%L::geometry,st_transform(geometry,4326))',NEW.original) INTO
NEW."utm_2.5";
    END IF;
    IF utm10 THEN
        EXECUTE FORMAT('SELECT st_transform(geometry,4326) FROM shared."utm_10x10" WHERE st_within(%L::geometry,st_transform(geometry,4326))',NEW.original) INTO NEW."utm_10";
    END IF;
    IF snap THEN
        EXECUTE FORMAT('SELECT st_SnapToGrid(%L::geometry,%L,%L)',NEW.original,snap_x,snap_y) INTO NEW."snap";
    END IF;
    IF snap_polygon THEN
        EXECUTE FORMAT('SELECT st_expand(st_SnapToGrid(%L::geometry,%L,%L),%L)',NEW.original,snap_x,snap_y,snap_polygon_size) INTO NEW."snap_polygon";
    END IF;

    RETURN NEW;
END IF;
IF tg_op = 'INSERT' THEN

    IF kef5 THEN
        EXECUTE FORMAT('SELECT geometry FROM shared."kef_5x5" WHERE st_within(%L::geometry,geometry)',NEW.original) INTO NEW."kef_5";
    END IF;
    IF kef10 THEN
        EXECUTE FORMAT('SELECT geometry FROM shared."kef_10x10" WHERE st_within(%L::geometry,geometry)',NEW.original) INTO NEW."kef_10";
    END IF;
    IF utm25 THEN
        EXECUTE FORMAT('SELECT st_transform(geometry,4326) as geom FROM shared."utm_2.5x2.5" WHERE st_within(%L::geometry,st_transform(geometry,4326))',NEW.original) INTO
NEW."utm_2.5";
    END IF;
    IF utm10 THEN
        EXECUTE FORMAT('SELECT st_transform(geometry,4326) FROM shared."utm_10x10" WHERE st_within(%L::geometry,st_transform(geometry,4326))',NEW.original) INTO NEW."utm_10";
    END IF;
    IF snap THEN
        EXECUTE FORMAT('SELECT st_SnapToGrid(%L::geometry,%L,%L)',NEW.original,snap_x,snap_y) INTO NEW."snap";
    END IF;
    IF snap_polygon THEN
        EXECUTE FORMAT('SELECT st_expand(st_SnapToGrid(%L::geometry,%L,%L),%L)',NEW.original,snap_x,snap_y,snap_polygon_size) INTO NEW."snap_polygon";
    END IF;

    RETURN NEW;
END IF;

END;

massive_edit

Allows you to edit the selected data massively on the file upload interface

Calls:

Functions:

General description:

Parameters:

download_restricted

Admin-controlled download authorization

Calls:

Functions:

General description:

Parameters:

job_manager (validation)

General description:

    * The job_manager (validation) module is used for managing the background processes of the project. It's parameters are the names of the jobs.
    * On the admin page you can set the time of running (simplified cron style: minute hour day), and the job parameters as json
    * Adding a new parameter will register the job in the jobs database table, and create the necessary template files in the modules/validation_modules, jobs folders.

Parameters:

    * The names of the background processes

Published jobs:

    observation_lists
        description:
            This job processes and copies the observation lists collected and uploaded by the mobile app. The observations land in a temporary table, where this job completes the obm_obsevation_list_id column, the columns of start, end and duration of list. If the uploaded list is not complete the list is skipped.

        parameters:
            * list_start_column (string): column name of list start
            * list_end_column (string): column name of list end
            * list_duration_column (string): column name of list duration
            * only_time (boolean): store whole timestamp or just time
            * time_as_int (boolean): convert time to minutes

            {
                "tablename": {
                    "list_start_column": "time_of_start",
                    "list_end_column": "time_of_end",
                    "list_duration_column": "duration",
                    "only_time": true,
                    "time_as_int": true
                    }
                }
            }

    incomplete_observation_lists
        description:
            If the uploaded list is incomplete, this module processes it. If the difference is smaller than the tolerance value, then the list will be uploaded by the next observation_list process, but a system message is sent. In other case, when the difference is larger than the tolerance only a system message is sent, the rest has to be processed manually.

        paraméterezés:
            * mail_to (int): role_id - who will get the messages
            * diff_tolerance (int): tolerance of difference
            * days_offset (int): number of days to wait until the list is processed

            {
                "tablename": {
                    "mail_to": 1265,
                    "diff_tolerance": 2,
                    "days_offset": 2
                }
            }




Calls:

Functions:

list_manager

Calls:

Functions:

General description:

Parameters:

move_project

Calls:

Functions:

General description:

Parameters: